RNAHelix: computational modeling of nucleic acid structures with Watson–Crick and non-canonical base pairs
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Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson–Crick or non-Watson–Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.
KeywordsMolecular modeling RNA Non Watson–Crick base pairs Base pair parameters Dinucleotide step parameters Electrostatic potential
This work has been supported by the Department of Atomic Energy, Govt. of India and Department of Biotechnology, Govt. of India. MB is recipient of J.C. Bose National Fellowship from DST, India.
- 7.Bhattacharya S, Mittal S, Panigrahi S, et al. (2015) RNABP COGEST: a resource for investigating functional RNAs. Database (Oxford) bav011. doi: 10.1093/database/bav011
- 30.Macke TJ, Case DA (1997) Modeling unusual nucleic acid structures. In: ACS Symp. Ser. pp 379–393Google Scholar
- 46.Rocchia W, Sridharan S, Nicholls A et al (2002) Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem 23:128–137. doi: 10.1002/jcc.1161 CrossRefGoogle Scholar
- 53.Leontis NB, Zirbel CL (2012) In: Leontis N, Westhof E (eds) Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking. Springer Berlin Heidelberg, Berlin, pp 281–298t;/bib>Google Scholar